MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : STM_v1_0 [2].
Target metabolite : gdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (108 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: STM3747 STM0051 STM2421 STM1749 STM2463 STM4275 STM1750 STM4570 STM2952 STM3709 STM0974 STM0152 STM0150 STM2317 STM4569 STM2338 STM2466 STM3968 STM3802 STM2196 STM3240 STM2970 STM3243 STM2971 STM1826   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.210278 (mmol/gDw/h)
  Minimum Production Rate : 0.163152 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 18.500000
  EX_glc__D_e : 5.000000
  EX_nh4_e : 3.133051
  EX_pi_e : 0.512784
  EX_k_e : 0.037345
  EX_so4_e : 0.025650
  EX_mg2_e : 0.001660
  EX_fe2_e : 0.001541
  EX_ca2_e : 0.000996
  EX_cl_e : 0.000996
  EX_cobalt2_e : 0.000664
  EX_cu2_e : 0.000664
  EX_mn2_e : 0.000664
  EX_mobd_e : 0.000664
  EX_zn2_e : 0.000664

Product: (mmol/gDw/h)
  EX_h2o_e : 25.868251
  EX_co2_e : 18.640948
  EX_h_e : 2.511844
  EX_etoh_e : 0.699620
  Auxiliary production reaction : 0.163152
  EX_ac_e : 0.062381
  EX_5dglcn_e : 0.008941
  EX_glyc__R_e : 0.005257
  DM_hmfurn_c : 0.000094

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
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